Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi2g712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04579 . .
Vvi2g714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g715 . . . . . . . . . . . . . . . . Cpe05g00159 . . . . . . . . . . . . . . . Cone12ag0487 . . . . . . Blo03g00880 . Bda07g00080 . . . . . . . . . . . . . . Bhi05g00449 . . Lac11g2448 . . . . . . . . . . . . . .
Vvi2g716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0489 . . . . . . Blo03g00881 . . . . Bpe11g00316 . . Sed01g4140 . . . . . . . . Bhi05g00448 Tan07g2008 Cmetu06g2068 Lac11g2449 Hepe06g0991 . Lcy12g1971 Cla09g01093 Cam09g1147 Cec09g1156 Cco09g1172 . . Cre09g1110 . . . .
Vvi2g717 . . . . . . . . Cmo06g00638 . Cma02g01632 . Car02g01391 . . . . . . . . . . . Cla10g00132 Cam10g0130 Cec10g0139 Cco10g0139 Clacu10g0135 Cmu10g0982 Cre10g0392 . . . . . . Chy04g00122 . . Blo19g00245 . . . . . . . Cmo02g01676 Cmo19g00231 Cma06g00631 . Car06g00565 . . Cpe15g00191 . . . . . . . . . . . . . . . . . Cme04g00145
Vvi2g718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g719 . . . . . . . . . Cmo16g01231 . . . . . Cpe14g00981 . . . . . . . . . . . . . . . Cone8ag0485 . . . Lsi07g01171 . . Cme06g02447 . Blo19g00246 . . Bpe08g00806 . . . . . . . Cma16g01181 . Car16g01115 . . . . . . . . . . . . . . . . . Csa03g00140 Chy06g02167 .
Vvi2g720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1027060 1031794 + Bda025138.1 Bda07g00080 80
5 9392029 9402338 + XM_039031872.1 Bhi05g00448 448
5 9392035 9402338 + XM_039031874.1 Bhi05g00449 449
3 34663264 34670992 - BLOR12061 Blo03g00880 880
3 34671059 34676251 - BLOR12062 Blo03g00881 881
19 12987645 12991094 - BLOR09588 Blo19g00245 245
19 13243760 13259816 - BLOR09589 Blo19g00246 246
8 10063978 10070040 - Bpe022926.1 Bpe08g00806 806
11 2313811 2318910 + Bpe003690.1 Bpe11g00316 316
9 12019995 12025186 + CaPI482276_09g011470.1 Cam09g1147 1147
10 2908328 2912819 - CaPI482276_10g001300.1 Cam10g0130 130
2 9146192 9149786 + Carg08858-RA Car02g01391 1391
6 3216703 3220046 - Carg23398-RA Car06g00565 565
16 9594155 9601435 + Carg23594-RA Car16g01115 1115
9 11395770 11400978 + CcPI632755_09g011720.1 Cco09g1172 1172
10 1324670 1329246 - CcPI632755_10g001390.1 Cco10g0139 139
9 11432534 11437697 + CePI673135_09g011560.1 Cec09g1156 1156
10 1332610 1337066 - CePI673135_10g001390.1 Cec10g0139 139
4 1103395 1107501 + Chy4G068400.1 Chy04g00122 122
6 25943311 25952805 + Chy6G126950.1 Chy06g02167 2167
10 1630157 1634697 - ClG42_10g0013500.10 Clacu10g0135 135
9 11640894 11651118 + ClCG09G011650.2 Cla09g01093 1093
10 1371990 1376560 - ClCG10G001320.1 Cla10g00132 132
2 9245371 9249271 + CmaCh02G016320.1 Cma02g01632 1632
6 3098366 3100917 - CmaCh06G006310.1 Cma06g00631 631
16 9041681 9049228 + CmaCh16G011810.1 Cma16g01181 1181
4 1097100 1102049 + MELO3C003436.2.1 Cme04g00145 145
6 31516896 31524396 - MELO3C013826.2.1 Cme06g02447 2447
6 29937499 29942834 - PI0025946.2 Cmetu06g2068 2068
2 9621080 9621909 + CmoCh02G016760.1 Cmo02g01676 1676
6 3197778 3201505 - CmoCh06G006380.1 Cmo06g00638 638
16 8818560 8827116 + CmoCh16G012310.1 Cmo16g01231 1231
19 1590103 1595192 - CmoCh19G002310.1 Cmo19g00231 231
10 1781283 1785810 - CmPI595203_10g009820.1 Cmu10g0982 982
8 3343402 3350885 - Conep08aG0050600.1 Cone8ag0485 485
12 3246133 3250158 - Conep12aG0050800.1 Cone12ag0487 487
12 3272508 3275833 + Conep12aG0051000.1 Cone12ag0489 489
5 834454 846945 + Cp4.1LG05g00280.1 Cpe05g00159 159
14 8287107 8295178 + Cp4.1LG14g09750.1 Cpe14g00981 981
15 1569966 1575132 - Cp4.1LG15g01860.1 Cpe15g00191 191
9 11590916 11596110 + CrPI670011_09g011100.1 Cre09g1110 1110
10 2744250 2748766 - CrPI670011_10g003920.1 Cre10g0392 392
3 1095869 1104501 - CsaV3_3G001400.1 Csa03g00140 140
3 39845652 39849433 + CsaV3_3G048850.1 Csa03g04579 4579
6 57655130 57665777 + Hsped.06g09910.1 Hepe06g0991 991
11 40678585 40679166 - Lag0033086.1 Lac11g2448 2448
11 40680254 40682490 - Lag0033087.1 Lac11g2449 2449
12 41099778 41105550 - Maker00038096 Lcy12g1971 1971
7 17195329 17208807 - Lsi07G011710.1 Lsi07g01171 1171
1 70190331 70202141 - Sed0013180.5 Sed01g4140 4140
7 71799668 71807873 - Tan0001284.1 Tan07g2008 2008
2 8337780 8347539 - Vvi2g712 Vvi2g712 712
2 8366138 8376971 + Vvi2g713 Vvi2g713 713
2 8381118 8408777 - Vvi2g714 Vvi2g714 714
2 8417887 8435103 + Vvi2g715 Vvi2g715 715
2 8468971 8483353 + Vvi2g716 Vvi2g716 716
2 8527797 8532588 - Vvi2g717 Vvi2g717 717
2 8572996 8573383 - Vvi2g718 Vvi2g718 718
2 8573733 8582220 - Vvi2g719 Vvi2g719 719
2 8613299 8613605 - Vvi2g720 Vvi2g720 720
2 8632907 8634857 - Vvi2g721 Vvi2g721 721
       

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